The sequencing of polynucleotides is a well established technique in molecular biology. Currently used procedures for sequencing are essentially as described in Sanger et al, Proc. Natl. Acad. Sci. USA 74:5463-5467 (1977) or Maxam et al., Methods in Enzymology 65:499-559, Academic Press, San Diego, Calif. (1980). Polynucleotide sequencing has become integral to virtually all aspects of molecular genetics. The Human Genome Project, and the sequencing of entire genomes from a variety of organisms has put great pressure on those researchers using conventional sequencing techniques. Additionally, the comparative sequencing of known genes for diagnostic purposes is expected to become increasingly important.
The amplification of polynucleotide sequences, typically through techniques such as PCR (polymerase chain reaction) is also a well established technique in molecular biology. The need for increased numbers of amplification reactions for genetic analysis, driven in part by the increased need for sequencing, has increased the need to perform large numbers of polynulceotide amplifications.
Given that the need for polynucleotide sequencing is rapidly increasing, there is ever growing pressure to reduce the time and costs associated with obtaining polynucleotide sequences. Many attempts have been made to perform sequencing in parallel, i.e., multiplex DNA sequencing. Methods of multiplex sequencing have been described in PCT application PUT/US96/09513, and U.S. Pat. No. 5,149,625. These techniques are either difficult to carry out, produce small amounts of sequence information, or do not provide significant savings of time or money. Similarly, established methods of multiplex PCR, e.g., as described in U.S. Pat. No. 5,582,989, are difficult to carry out on a large scale.
Conventional sequencing methods are impractical for high throughput sequencing because of numerous reasons such as the cost of reagents and the large number of sample handling steps required. Similarly, conventional polynucleotide amplification methods are impractical for high throughput sequencing for numerous reasons such as the cost of reagents and the large number of sample handling steps required. The inventions described herein may be used to both increase the amount of genetic information obtained in a given period of time and to decrease the costs of obtaining the genetic information.